Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms

(2017) Marta M. Fay et al.   JOURNAL OF MOLECULAR BIOLOGY

Translation of CircRNAs

(2017) Nagarjuna Reddy Pamudurti et al.   MOLECULAR CELL

Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis

(2017) Ivano Legnini et al.   MOLECULAR CELL

Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide

(2017) Zhen Shi et al.   MOLECULAR CELL

Chemical and structural effects of base modifications in messenger RNA

(2017) Emily M. Harcourt et al.   NATURE

DNA G-quadruplexes in the human genome: detection, functions and therapeutic potential

(2017) Robert Hänsel-Hertsch et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA structure inference through chemical mapping after accidental or intentional mutations

(2017) Clarence Y. Cheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

(2017) Zhichao Miao et al.   RNA

The RNA Epistructurome: Uncovering RNA Function by Studying Structure and Post-Transcriptional Modifications

(2017) Danny Incarnato et al.   TRENDS IN BIOTECHNOLOGY

An Ancient Pseudoknot in TNF-α Pre-mRNA Activates PKR, Inducing eIF2α Phosphorylation that Potently Enhances Splicing

(2017) Lise Sarah Namer et al.   Cell Reports

Genome-Wide Maps of m6A circRNAs Identify Widespread and Cell-Type-Specific Methylation Patterns that Are Distinct from mRNAs

(2017) Chan Zhou et al.   Cell Reports

The Human CCHC-type Zinc Finger Nucleic Acid-Binding Protein Binds G-Rich Elements in Target mRNA Coding Sequences and Promotes Translation

(2017) Daniel Benhalevy et al.   Cell Reports

Operon mRNAs are organized into ORF-centric structures that predict translation efficiency

(2017) David H Burkhardt et al.   eLife

Genome-Wide Analysis of RNA Secondary Structure

(2016) Philip C. Bevilacqua et al.   Annual Review of Genetics

More than just scanning: the importance of cap-independent mRNA translation initiation for cellular stress response and cancer

(2016) Rafaela Lacerda et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

A novel translational control mechanism involving RNA structures within coding sequences

(2016) Jennifer Jungfleisch et al.   GENOME RESEARCH

nanoCAGE reveals 5′ UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs

(2016) Valentina Gandin et al.   GENOME RESEARCH

Irregular G-quadruplexes Found in the Untranslated Regions of Human mRNAs Influence Translation

(2016) François Bolduc et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RNA Sequence Context Effects Measured In Vitro Predict In Vivo Protein Binding and Regulation

(2016) J. Matthew Taliaferro et al.   MOLECULAR CELL

The m 6 A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells

(2016) Shuibin Lin et al.   MOLECULAR CELL

eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation

(2016) Amy S. Y. Lee et al.   NATURE

The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA

(2016) Dan Dominissini et al.   NATURE

Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor

(2016) Shintaro Iwasaki et al.   NATURE

Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

(2016) Viviana I. Risca et al.   NATURE

A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs

(2016) Elena Rivas et al.   NATURE METHODS

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

(2016) Meghan Zubradt et al.   NATURE METHODS

The roles of RNA processing in translating genotype to phenotype

(2016) Kassie S. Manning et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Post-transcriptional gene regulation by mRNA modifications

(2016) Boxuan Simen Zhao et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

N6-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics

(2016) Junhong Choi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identification of consensus binding sites clarifies FMRP binding determinants

(2016) Bart R. Anderson et al.   NUCLEIC ACIDS RESEARCH

eIF4B stimulates translation of long mRNAs with structured 5′ UTRs and low closed-loop potential but weak dependence on eIF4G

(2016) Neelam Dabas Sen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA structure through multidimensional chemical mapping

(2016) Siqi Tian et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

(2016) B. Delatte et al.   SCIENCE

Visualizing the molecular sociology at the HeLa cell nuclear periphery

(2016) J. Mahamid et al.   SCIENCE

Translational control by 5'-untranslated regions of eukaryotic mRNAs

(2016) A. G. Hinnebusch et al.   SCIENCE

Systematic discovery of cap-independent translation sequences in human and viral genomes

(2016) Shira Weingarten-Gabbay et al.   SCIENCE

N6-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics

(2016) Junhong Choi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

An Independently Folding RNA G-Quadruplex Domain Directly Recruits the 40S Ribosomal Subunit

(2015) Debmalya Bhattacharyya et al.   BIOCHEMISTRY

Detection of RNA–Protein Interactions in Living Cells with SHAPE

(2015) Matthew J. Smola et al.   BIOCHEMISTRY

The role of IRES trans-acting factors in carcinogenesis

(2015) Mame Daro Faye et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Cap-dependent, scanning-free translation initiation mechanisms

(2015) Ora Haimov et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Targeting the eIF4A RNA helicase as an anti-neoplastic approach

(2015) Jennifer Chu et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Reprogramming the genetic code: The emerging role of ribosomal frameshifting in regulating cellular gene expression

(2015) Vivek M. Advani et al.   BIOESSAYS

5′ UTR m6A Promotes Cap-Independent Translation

(2015) Kate D. Meyer et al.   CELL

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

(2015) Xiao Wang et al.   CELL

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation

(2015) Shengdong Ke et al.   GENES & DEVELOPMENT

Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A

(2015) Neelam Dabas Sen et al.   GENOME RESEARCH

The Ribosome Challenge to the RNA World

(2015) Jessica C. Bowman et al.   JOURNAL OF MOLECULAR EVOLUTION

Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification

(2015) Caroline Roost et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

eIF3 targets cell-proliferation messenger RNAs for translational activation or repression

(2015) Amy S. Y. Lee et al.   NATURE

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Dynamic m6A mRNA methylation directs translational control of heat shock response

(2015) Jun Zhou et al.   NATURE

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

Progress and challenges for chemical probing of RNA structure inside living cells

(2015) Miles Kubota et al.   Nature Chemical Biology

Stabilization of the G-quadruplex at the VEGF IRES represses cap-independent translation

(2015) Anne Cammas et al.   RNA Biology

The RNA structurome: transcriptome-wide structure probing with next-generation sequencing

(2015) Chun Kit Kwok et al.   TRENDS IN BIOCHEMICAL SCIENCES

The malignant phenotype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape

(2015) A Modelska et al.   Cell Death & Disease

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

(2015) Rui Fang et al.   PLoS Genetics

The Scanning Mechanism of Eukaryotic Translation Initiation

(2014) Alan G. Hinnebusch   Annual Review of Biochemistry

Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genomes

(2014) Sean R. Eddy   Annual Review of Biophysics

Fragile X Mental Retardation Protein Regulates Translation by Binding Directly to the Ribosome

(2014) Eileen Chen et al.   MOLECULAR CELL

Quantitative analysis of mammalian translation initiation sites by FACS-seq

(2014) W. L. Noderer et al.   Molecular Systems Biology

RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation

(2014) Shifeng Xue et al.   NATURE

Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

(2014) Ashton Trey Belew et al.   NATURE

RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer

(2014) Andrew L. Wolfe et al.   NATURE

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

Insights into RNA structure and function from genome-wide studies

(2014) Stefanie A. Mortimer et al.   NATURE REVIEWS GENETICS

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

Single-molecule correlated chemical probing of RNA

(2014) P. J. Homan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states

(2014) Siqi Tian et al.   RNA

Gene regulation by structured mRNA elements

(2014) Andreas Wachter   TRENDS IN GENETICS

Hypoxia Induces VEGF-C Expression in Metastatic Tumor Cells via a HIF-1α-Independent Translation-Mediated Mechanism

(2014) Florent Morfoisse et al.   Cell Reports

Translational Regulation of Specific mRNAs Controls Feedback Inhibition and Survival during Macrophage Activation

(2014) Johanna Schott et al.   PLoS Genetics

Evidence for a Functionally Relevant Rocaglamide Binding Site on the eIF4A–RNA Complex

(2013) Heather Sadlish et al.   ACS Chemical Biology

High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis

(2013) Schraga Schwartz et al.   CELL

A perspective on mammalian upstream open reading frame function

(2013) Joanna Somers et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Overexpression of FGF9 in colon cancer cells is mediated by hypoxia-induced translational activation

(2013) T.-M. Chen et al.   NUCLEIC ACIDS RESEARCH

Tuning gene expression with synthetic upstream open reading frames

(2013) J. P. Ferreira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Current Status of Vertebrate Cellular mRNA IRESs

(2013) R. J. Jackson   Cold Spring Harbor Perspectives in Biology

Before It Gets Started: Regulating Translation at the 5′ UTR

(2012) Patricia R. Araujo et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

RNA Binding Protein/RNA Element Interactions and the Control of Translation

(2012) Xavier Pichon et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Posttranscriptional Gene Regulation by Long Noncoding RNA

(2012) Je-Hyun Yoon et al.   JOURNAL OF MOLECULAR BIOLOGY

Systematic discovery of structural elements governing stability of mammalian messenger RNAs

(2012) Hani Goodarzi et al.   NATURE

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat

(2012) Claudia Carrieri et al.   NATURE

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

5'-UTR RNA G-quadruplexes: translation regulation and targeting

(2012) A. Bugaut et al.   NUCLEIC ACIDS RESEARCH

Aberrant expression of c-Jun in glioblastoma by internal ribosome entry site (IRES)-mediated translational activation

(2012) L. Blau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanisms and implications of programmed translational frameshifting

(2012) Jonathan D. Dinman   Wiley Interdisciplinary Reviews-RNA

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Ribosome-Mediated Specificity in Hox mRNA Translation and Vertebrate Tissue Patterning

(2011) Nadya Kondrashov et al.   CELL

FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism

(2011) Jennifer C. Darnell et al.   CELL

Cellular IRES-mediated translation

(2011) Anton A Komar et al.   CELL CYCLE

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

(2011) B. J. Parker et al.   GENOME RESEARCH

Duplex Unwinding and ATPase Activities of the DEAD-Box Helicase eIF4A Are Coupled by eIF4G and eIF4B

(2011) Ali R. ze et al.   JOURNAL OF MOLECULAR BIOLOGY

rRNA Pseudouridylation Defects Affect Ribosomal Ligand Binding and Translational Fidelity from Yeast to Human Cells

(2011) Karen Jack et al.   MOLECULAR CELL

A two-dimensional mutate-and-map strategy for non-coding RNA structure

(2011) Wipapat Kladwang et al.   Nature Chemistry

mRNA helicases: the tacticians of translational control

(2011) Armen Parsyan et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The role of IREStrans-acting factors in regulating translation initiation

(2010) Helen A. King et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The role of G-quadruplex in RNA metabolism: Involvement of FMRP and FMR2P

(2010) Mireille Melko et al.   BIOCHIMIE

Regulation of innate immunity through RNA structure and the protein kinase PKR

(2010) Subba Rao Nallagatla et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

An RNA G-Quadruplex Is Essential for Cap-Independent Translation Initiation in Human VEGF IRES

(2010) Mark J. Morris et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Human Cytomegalovirus Induces the Endoplasmic Reticulum Chaperone BiP through Increased Transcription and Activation of Translation by Using the BiP Internal Ribosome Entry Site

(2010) N. J. Buchkovich et al.   JOURNAL OF VIROLOGY

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

(2010) Calvin H. Jan et al.   NATURE

The mechanism of eukaryotic translation initiation and principles of its regulation

(2010) Richard J. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

5'-UTR G-quadruplex structures acting as translational repressors

(2010) J.-D. Beaudoin et al.   NUCLEIC ACIDS RESEARCH

Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast

(2010) Ashton T. Belew et al.   NUCLEIC ACIDS RESEARCH

Upregulated c-myc expression in multiple myeloma by internal ribosome entry results from increased interactions with and expression of PTB-1 and YB-1

(2010) L C Cobbold et al.   ONCOGENE

Riboswitches and the RNA World

(2010) R. R. Breaker   Cold Spring Harbor Perspectives in Biology

Cap and cap-binding proteins in the control of gene expression

(2010) Ivan Topisirovic et al.   Wiley Interdisciplinary Reviews-RNA

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs

(2009) D. M. Landry et al.   GENES & DEVELOPMENT

The hnRNA-Binding Proteins hnRNP L and PTB Are Required for Efficient Translation of the Cat-1 Arginine/Lysine Transporter mRNA during Amino Acid Starvation

(2009) M. Majumder et al.   MOLECULAR AND CELLULAR BIOLOGY

Dynamic refolding of IFN-γ mRNA enables it to function as PKR activator and translation template

(2009) Smadar Cohen-Chalamish et al.   Nature Chemical Biology

Predictable suppression of gene expression by 5′-UTR-based RNA quadruplexes

(2009) Kangkan Halder et al.   NUCLEIC ACIDS RESEARCH

IRESite—a tool for the examination of viral and cellular internal ribosome entry sites

(2009) Martin Mokrejš et al.   NUCLEIC ACIDS RESEARCH

Antitumor Activity and Mechanism of Action of the Cyclopenta[b]benzofuran, Silvestrol

(2009) Regina Cencic et al.   PLoS One

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

(2009) S. E. Calvo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origins and evolution of the mechanisms regulating translation initiation in eukaryotes

(2009) Greco Hernández et al.   TRENDS IN BIOCHEMICAL SCIENCES

RNA pseudoknots and the regulation of protein synthesis

(2008) Ian Brierley et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Position and Stability Are Determining Factors for Translation Repression by an RNA G-Quadruplex-Forming Sequence within the 5′ UTR of theNRASProto-oncogene†

(2008) Sunita Kumari et al.   BIOCHEMISTRY

Translation Initiation on Mammalian mRNAs with Structured 5′UTRs Requires DExH-Box Protein DHX29

(2008) Vera P. Pisareva et al.   CELL

An upstream open reading frame within an IRES controls expression of a specific VEGF-A isoform

(2008) Amandine Bastide et al.   NUCLEIC ACIDS RESEARCH

The G-quartet containing FMRP binding site in FMR1 mRNA is a potent exonic splicing enhancer

(2008) Marie-Cécile Didiot et al.   NUCLEIC ACIDS RESEARCH

FGF2 Translationally Induced by Hypoxia Is Involved in Negative and Positive Feedback Loops with HIF-1α

(2008) Caroline Conte et al.   PLoS One

Splicing mediates the activity of four putative cellular internal ribosome entry sites

(2008) B. T. Baranick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potent activation of FGF-2 IRES-dependent mechanism of translation during brain development

(2008) S. Audigier et al.   RNA

Inhibition of translation in living eukaryotic cells by an RNA G-quadruplex motif

(2008) A. Arora et al.   RNA

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Re-programming of translation following cell stress allows IRES-mediated translation to predominate

(2007) Keith A. Spriggs et al.   BIOLOGY OF THE CELL